How it feels in a cell

M Bonucci, T Shu, LJ Holt - Trends in Cell Biology, 2023 - cell.com
Life emerges from thousands of biochemical processes occurring within a shared
intracellular environment. We have gained deep insights from in vitro reconstitution of …

The rich inner life of the cell nucleus: dynamic organization, active flows, and emergent rheology

A Zidovska - Biophysical Reviews, 2020 - Springer
The cell nucleus stores the genetic material essential for life, and provides the environment
for transcription, maintenance, and replication of the genome. Moreover, the nucleoplasm is …

[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization

X Lin, Y Qi, AP Latham, B Zhang - The Journal of chemical physics, 2021 - pubs.aip.org
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …

Euchromatin activity enhances segregation and compaction of heterochromatin in the cell nucleus

A Mahajan, W Yan, A Zidovska, D Saintillan… - Physical Review X, 2022 - APS
The large-scale organization of the genome inside the cell nucleus is critical for the cell's
function. Chromatin—the functional form of DNA in cells—serves as a template for active …

Interphase chromatin undergoes a local sol-gel transition upon cell differentiation

I Eshghi, JA Eaton, A Zidovska - Physical review letters, 2021 - APS
Cell differentiation, the process by which stem cells become specialized cells, is associated
with chromatin reorganization inside the cell nucleus. Here, we measure the chromatin …

Nucleus mechanosensing in cardiomyocytes

IL Coscarella, M Landim-Vieira… - International Journal of …, 2023 - mdpi.com
Cardiac muscle contraction is distinct from the contraction of other muscle types. The heart
continuously undergoes contraction–relaxation cycles throughout an animal's lifespan. It …

Activity-driven phase transition causes coherent flows of chromatin

I Eshghi, A Zidovska, AY Grosberg - Physical Review Letters, 2023 - APS
We discover a new type of nonequilibrium phase transition in a model of chromatin
dynamics, which accounts for the coherent motions that have been observed in experiment …

The power of weak, transient interactions across biology: A paradigm of emergent behavior

PA Vasquez, B Walker, K Bloom, D Kolbin… - Physica D: Nonlinear …, 2023 - Elsevier
A growing list of diverse biological systems and their equally diverse functionalities provides
realizations of a paradigm of emergent behavior. In each of these biological systems …

Dynamical phase transition in models that couple chromatin folding with histone modifications

A Sood, G Schuette, B Zhang - Physical Review E, 2024 - APS
Genomic regions can acquire heritable epigenetic states through unique histone
modifications, which lead to stable gene expression patterns without altering the underlying …

Conformations, correlations, and instabilities of a flexible fiber in an active fluid

S Weady, DB Stein, A Zidovska, MJ Shelley - Physical Review Fluids, 2024 - APS
Fluid-structure interactions between active and passive components are important for many
biological systems to function. A particular example is chromatin in the cell nucleus, where …